Typing tool
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Typing tool
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Complete norovirus genomes
| OP205558 | GII.4 Sydney | |
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| GII.P16 |
ORF1: 1..5082
ORF2: 5063..6685
ORF3: 6685..7491
LOCUS OP205558 7491 bp RNA linear VRL 21-JUN-2023
DEFINITION Norovirus GII isolate RIVM-NOV-2018-0407_R03-13 nonstructural
polyprotein (ORF1) gene, partial cds; and VP1 (ORF2) and VP2 (ORF3)
genes, complete cds.
ACCESSION OP205558
VERSION OP205558.1
KEYWORDS .
SOURCE Norovirus GII
ORGANISM Norovirus GII
Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
Picornavirales; Caliciviridae; Norovirus; Norwalk virus.
REFERENCE 1 (bases 1 to 7491)
AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T.,
Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.
TITLE Shotgun whole genome sequencing for gastroenteritis surveillance
using Norovirus as a model
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 7491)
AUTHORS Schmitz,D., Zwagemaker,F., van der Veer,B., Vennema,H., Bosch,T.,
Laros,J.F., Koopmans,M.P., de Graaf,M. and Kroneman,A.
TITLE Direct Submission
JOURNAL Submitted (05-AUG-2022) Center for Infectious Diseases,
Rijksinstituut voor Volksgezondheid en Milieu, Antonie van
Leeuwenhoeklaan 9, Bilthoven, Utrecht 3721 MA, Netherlands
COMMENT ##Assembly-Data-START##
Assembly Method :: SPAdes v. v3.11.0
Sequencing Technology :: Illumina
##Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..7491
/organism="Norovirus GII"
/mol_type="genomic RNA"
/isolate="RIVM-NOV-2018-0407_R03-13"
/isolation_source="Human feces"
/host="Homo sapiens"
/db_xref="taxon:122929"
/country="Netherlands"
/collection_date="2018-10-22"
/note="genotype: GII.4 Sydney[P16]"
gene <1..5082
/gene="ORF1"
CDS <1..5082
/gene="ORF1"
/codon_start=1
/product="nonstructural polyprotein"
/protein_id="UUV60975.1"
/translation="DATVAVACNNNNDKEKSSGEGLFTNMSSTLKKALGARPKQPAPR
DEPQKPPRPPTPELVKRIPPPPPNGEEEEEPVIRYEVKSGISGLPELTTVPQPDVANT
AFSVPPLSLRENREAKEPLTGAILEMWDGEIYHYGLYVEKGLVLGVHKPPAAISMARV
ELTPLSLYWRVVYTPQYLISPETLRRLNGEAFPYTAFDNNCYAFCCWVLDLNDSWLSR
RMVQRTTGFFRPYQEWNRKPLPTMDDSKIKKVANIFLCSLSTLFTRPIKDLIGKIKPL
NMLNILATCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDYELQGPEDLAVE
LVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFPKKEE
ANELAMVRAIEDAVLDLEAIENNHMTTLLKDKDSLATYMKTLDMEEEKARRLSTKSAS
PDIVGTINALLARIAAARSLVHRAKEELSSRMRPVVVMISGKPGIGKTHLAREVARKV
ASTLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRIQELADTCPLTL
NCDRIENKGKVFDSEVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEKAKRD
FPGQPDMWKDAFKPDFSHIKLQLAPQGGFDKNGNTPHGKGVMKTLTTGSLIARASGLL
HERMDEFELQGPTTTTFNFDRNRITAFRQLAAENKYGLVDTMKVGNQLKGVKTMEELK
QAIRNVTIKRCRIIYGGSTYDLESDGKGKVLVEKVKNTSVQTNNELAGALHHLKHARI
RYYVKCVQEAVYSIIQIAGAAFVTTRIARRMNIQELWSKPQLDQNESEAREEAPKSED
DEFIISSKDIKEEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNGKYSIEE
YLQDRDRYYEELAIAKATEEDFCEEEEIKIRQRIFRPTRKQRKEERATLGLVTGSEIR
KRNPDDFKPKGKLWADDNRSVDYNEKLDFEAPPSIWSRIVSFGSGWGFWVSPSLFITS
THVIPAGITEAFGVSIKQIQIHKSGEFCRFRFPKPIRPDVTGMILEEGAPEGTVATVL
IKRPTGELMPLAARMGTHATMKIQGRMVGGQMGMLLTGSNAKGMDLGTTPGDCGCPYI
YKRGNDYIVIGVHTAAARGGNTVICATQGSEGEATLEGGDDKGTYCGAPILGPGGAPK
LSTKTKFWRSSNTPLPPGTYEPAYLGGRDPRVKGGPSLQQVMRDQLKPFTEPRGKPPR
PSVLEAAKQTIINVLEQTLDPPQKWTYAQACASLDKTTSSGHPHHVRKNEFWNGETFT
GKLADQASKANLMFEEGKHMTPVYTAALKDELVKTEKIYGKIKKRLLWGSDLSTMIRC
ARSFGGLMDEMKAHCISLPVRVGMNMNEDGPIIFEKHSRYKYHYDADYSRWDSTQQRA
VLAAALEIMVRFSAEPQLAQIVAEDLLAPSVVDVGDFKITINEGLPSGVPCTSQWNSI
AHWLLTLCALSEVTKLSPDIIQANSMFSFYGDDEIVSTDIKLDPEQLTAKLKEYGLKP
TRPDKTEGPLIISEDLNGLTFLRRTVTRDPAGWFGKLDQSSILRQMYWTRGPNHEDPN
ETMIPHSQRPIQLMALLGEASLHGPSFYSRISKLVITELKEGGMDFYVPRQEPMFRWM
RFSDLSTWEGDRNLAPNFVNEDGVE"
mat_peptide <1..978
/gene="ORF1"
/product="p48"
mat_peptide 979..2076
/gene="ORF1"
/product="NTPase"
mat_peptide 2077..2607
/gene="ORF1"
/product="p22"
mat_peptide 2608..3006
/gene="ORF1"
/product="VPg"
mat_peptide 3007..3549
/gene="ORF1"
/product="Pro"
mat_peptide 3550..5079
/gene="ORF1"
/product="RdRp"
gene 5063..6685
/gene="ORF2"
CDS 5063..6685
/gene="ORF2"
/note="major capsid protein"
/codon_start=1
/product="VP1"
/protein_id="UUV60976.1"
/translation="MKMASSDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
QNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGG
FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
VRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
TVESRTKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
QLSPVNICTFRGDVTHITGSRNYTMNLASQNWNNYDPTEEIPAPLGTPDFAGKIQGML
TQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDHDFEANQNTKFTPVGVIQDG
STTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLD
CLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAV"
gene 6685..7491
/gene="ORF3"
CDS 6685..7491
/gene="ORF3"
/note="minor structural protein; small basic protein"
/codon_start=1
/product="VP2"
/protein_id="UUV60977.1"
/translation="MAGAFFAGLASDVLGSGLGSLINAGAGAINQKVEFENNRKLQQA
SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFSETDAARGAIN
APMTKALDWSGTRYWAPDARITTYNAGHFSTPQPSRALPGRANLRDAVPARGPSNKSS
NSSTVTSVYSNQTISTRLGSTAGSGTSVSSLPSTARTRSWVEDQNRNLSPFMRGAHNI
SFVTPPSSRSSSQGTVSTVPKEILDSWTGAFNTRRQPLFAHIRKRGESRV"
ORIGIN
1 gacgctaccg ttgccgttgc ttgcaacaac aacaacgaca aggaaaaatc ttcaggtgaa
61 ggcttattca caaatatgtc ttccacctta aagaaagccc tcggggctag gcccaaacag
121 cctgccccga gagacgaacc acaaaagccc ccaagaccac caactcccga gttggtcaag
181 aggatacccc ctcctccacc taatggcgaa gaagaagaag aaccagtaat taggtatgag
241 gtcaagagtg gaatctctgg cctgcccgag ctcacaacag tcccccaacc ggacgtggcc
301 aacacagcat tcagtgttcc accactgagc ttgagagaaa acagggaggc caaggaaccg
361 ctaacagggg caatattaga gatgtgggat ggagagatat accactatgg cctgtacgtg
421 gagaaaggct tagtgttggg tgtgcacaaa ccacctgcag ccataagcat ggcaagagtg
481 gagttgacgc cgctgtcatt gtactggcgt gtggtgtaca ctccccaata cctcatctcc
541 cctgaaactc tcaggaggct caacggagag gcgttccctt acaccgcctt cgacaacaac
601 tgctacgcct tttgctgctg ggtgttagac ctcaatgact catggcttag caggaggatg
661 gtgcaaagaa cgacgggctt cttcagacct taccaagagt ggaacagaaa acccctgccc
721 accatggatg actccaaaat aaagaaggta gcaaatatat tcctatgttc attgtccaca
781 ttattcacca gacccataaa agacctcata ggaaaaatta aaccattaaa catgttgaac
841 atcctggcaa cgtgtgactg gacgtttgcc ggaatagtgg agtctctgat attacttgct
901 gaactcttcg gagttttctg gacaccccca gatgtgtctg ctatgatcgc tcccttactc
961 ggggactacg agttgcaagg gccagaagac ctcgccgttg aactcgtacc tgtggtaatg
1021 ggagggattg gtttggtgtt gggattcacc aaagagaaaa ttggcaaaat gttgtcctca
1081 gcagcatcaa cactcagggc ttgcaaagat cttggtgcct atggcttaga gatactcaaa
1141 ttagtcatga agtggttctt cccaaagaaa gaggaggcca atgagctagc catggtgagg
1201 gccatagagg atgccgtact agatcttgag gcaatagaaa ataaccacat gacaaccctg
1261 ttgaaagaca aagacagctt agcaacatac atgaaaacac tggacatgga ggaggagaaa
1321 gccagaaggt tgtccacaaa atctgcatcc cctgacatag ttgggacaat caacgccctg
1381 ctggctcgaa tagcagcagc caggtcatta gtccacaggg ccaaggaaga gctatctagt
1441 aggatgagac cagtagttgt tatgatatct ggtaaaccag gaataggcaa aactcatctg
1501 gccagggaag tggcaagaaa ggtggcatcc actctcacag gggatcaaag agtcggactc
1561 ataccaagaa acggtgtgga ccattgggat gcatataaag gtgagagagt cgtgctgtgg
1621 gacgactatg gcatgagtaa ccccattcat gatgctcttc gcatacaaga attggctgat
1681 acgtgtcccc ttaccttaaa ttgtgacaga attgaaaata agggaaaagt ttttgacagt
1741 gaagtcataa taatcacaac aaaccttgcc aacccagccc cacttgatta tgtcaacttt
1801 gaggcctgtt ccaggagaat tgatttcctg gtgtacgctg aggcaccaga agtagaaaag
1861 gcaaaacggg attttcctgg tcagccagat atgtggaagg acgccttcaa gccggacttt
1921 tcacacatca agctacagct tgcacctcag ggcggctttg acaagaatgg taacacccca
1981 catgggaaag gggtgatgaa gaccctcact accggttctc tgattgcccg tgcatcaggc
2041 ctactgcatg agaggatgga tgaatttgaa ctccaaggtc ccacaaccac taccttcaat
2101 ttcgaccgga acagaatcac agcattcaga caattggctg cagaaaacaa gtatggattg
2161 gtggacacca tgaaagttgg caatcaacta aaaggagtga aaaccatgga agaactcaaa
2221 caagcaatca ggaatgtgac catcaagagg tgccggatca tctacggtgg ctccacgtat
2281 gaccttgaat ctgatggcaa gggcaaagtt ttggtggaaa aggtcaagaa cacctctgta
2341 cagaccaaca acgagttggc cggggccctg caccacctca aacacgcccg aatcaggtac
2401 tatgtcaaat gtgtgcaaga agcagtctat tccatcatac aaattgccgg cgctgcgttt
2461 gtcaccacgc gtatcgcacg ccgcatgaac atacaagaac tctggtcgaa gccacaatta
2521 gatcaaaatg aatcagaggc tagggaagag gcccccaagt cagaagatga cgagttcatc
2581 atatcttcta aggacatcaa ggaggaagga aagaagggca aaaacaaaac tggccgtggc
2641 aagaaacaca ctgcattctc cagcaagggc ttgagcgatg aggagtatga cgagtacaag
2701 aggataaggg aagagagaaa tgggaagtac tctatagagg agtatcttca agacagagac
2761 aggtactatg aggagctcgc cattgccaag gccacggaag aagacttctg tgaagaggag
2821 gagatcaaaa tccgtcagag aattttccgt cccaccagga aacaaagaaa ggaagagagg
2881 gccacattag ggctggtaac aggttcagaa atcagaaaaa gaaaccctga tgacttcaaa
2941 cccaaaggga agctgtgggc cgatgacaac agaagtgttg actacaatga gaaactggac
3001 tttgaggccc ccccaagcat atggtctagg attgtgagct ttggttctgg ctggggcttc
3061 tgggtatcac caagcctgtt cataacatca actcatgtaa tccccgcagg cataacagaa
3121 gcatttggag tctccatcaa acaaattcag atccacaaat caggtgaatt ttgccgattc
3181 agattcccaa aaccaatcag accagatgtg acaggaatga tcttggaaga aggtgcgcct
3241 gaaggcaccg tagcaaccgt gctcatcaaa cgccccaccg gagagctcat gcctcttgca
3301 gccagaatgg ggacacacgc aaccatgaaa attcaaggcc gcatggttgg cggacagatg
3361 ggtatgttgc tcactggatc aaatgctaaa ggaatggatt tgggaacaac tcctggtgac
3421 tgtggctgtc cttacatcta taaaaggggc aatgactata tagtcattgg ggtgcacact
3481 gcagcagccc gtggtggaaa caccgtcatc tgtgccacac agggaagtga gggtgaggca
3541 actcttgagg gtggagacga caaaggaaca tactgtgggg cacccatttt aggccctggg
3601 ggtgcaccaa aattgagcac caaaaccaaa ttttggaggt catcgaacac gccccttcca
3661 ccagggacat atgagcctgc ctacctcggt ggccgtgatc cacgcgtcaa gggtgggccc
3721 tccttgcagc aggtaatgag agaccagttg aagccattca ctgaacccag gggcaaacct
3781 ccaaggccaa gtgtattgga agcagccaaa caaaccatta tcaatgttct cgaacaaacc
3841 ctggaccctc cacaaaaatg gacatacgca caggcgtgtg cctcacttga taaaaccacc
3901 tccagcgggc atccccatca cgtccgaaag aatgaattct ggaatggtga gaccttcaca
3961 ggtaaattgg cagaccaagc atcaaaagca aacctaatgt ttgaggaagg gaaacacatg
4021 acaccagtgt atacagcagc actcaaggac gagctagtca agactgagaa aatctatgga
4081 aagatcaaga agagactgct ctggggctct gacttgtcca ccatgatccg gtgcgctagg
4141 tcatttggtg ggctcatgga cgagatgaaa gcacactgca tatcactccc agtacgagtt
4201 ggcatgaata tgaatgaaga tggtccaata atatttgaga aacattccag atacaaatac
4261 cattatgatg cagactactc tcgttgggat tcaacacaac agagggcagt actagcagca
4321 gccttggaaa tcatggtcag attctctgca gaaccacaat tggcacaaat agtcgctgag
4381 gatctactgg cccctagtgt agtagatgta ggagatttta aaatcacaat aaatgaaggg
4441 ctcccatctg gcgtgccgtg cacttctcaa tggaactcca ttgcacactg gctgctaact
4501 ctctgtgcct tgtctgaagt caccaaactg tcccctgaca tcatacaagc aaattccatg
4561 ttctcatttt acggtgatga cgagattgtc agcaccgaca taaaattgga ccctgaacag
4621 ttaaccgcca agttgaagga gtacggcctg aaaccaaccc gcccagacaa gaccgagggg
4681 cccctgatca tcagtgaaga tttgaacgga ctcactttcc tccgaaggac ggtgactcgt
4741 gacccagctg gctggtttgg aaagctggac caaagttcaa ttttgaggca gatgtactgg
4801 actagaggac caaaccatga agaccccaat gagacaatga taccccattc tcaaagaccc
4861 atacagctca tggcactgct tggtgaagcc tctcttcacg gaccctcttt ctacagtaga
4921 attagtaaat tggtcataac tgaactcaaa gaaggtggga tggactttta cgtgccaagg
4981 caggaaccca tgttcaggtg gatgaggttt tctgacttga gcacgtggga gggcgatcgc
5041 aatctggctc ccaattttgt gaatgaagat ggcgtcgagt gacgccaacc catctgatgg
5101 gtccgcagcc aacctcgtac cagaggtcaa caatgaggtt atggctttgg agcccgttgt
5161 tggtgccgct attgcggcac ctgtagcggg ccaacaaaat gtaattgacc cctggattag
5221 aaataatttt gtacaagccc ctggtgggga gtttacagtg tcccctagaa acgctccagg
5281 tgaaatacta tggagcgcgc ccctaggccc tgacctaaat ccctacctat cccatttggc
5341 cagaatgtac aatggttatg caggtggttt tgaagtgcag gtaattctcg cggggaacgc
5401 gttcaccgcc gggaagatta tatttgcagc agtcccacca aattttccaa ctgaaggctt
5461 aagtcctagc caggtcacta tgttccccca tataatagta gatgttagac aattagaacc
5521 tgtgctgatt cccttacctg atgttaggaa taatttctat cattacaatc agtcaaatga
5581 tcccactatc aagttgatag caatgttgta tacaccactt agggctaata atgcaggaga
5641 tgatgttttc acagtttcgt gccgagttct cacgagacca tcccccgatt ttgatttcat
5701 atttttagtg ccacccacag ttgagtcaag aactaaacca ttctctgtcc cagttttaac
5761 tgttgaggag atgaccaatt caagattccc catccctttg gaaaagttgt tcacaggccc
5821 cagcagtgcc tttgttgttc aaccacaaaa cggcaggtgc acaactgatg gcgtgctcct
5881 aggcaccacc caactttctc ctgtcaacat ctgcaccttc agaggggatg tcacccacat
5941 cacaggcagt cgcaactaca caatgaattt ggcttctcaa aattggaaca actatgaccc
6001 aacagaagaa atcccagccc ctctaggaac tccagatttt gcagggaaga ttcaaggcat
6061 gctcacccaa accacaagga cagacggttc aacacgcggc cacaaagcta cagtgtacac
6121 tgggagcgcc gactttgctc caaaactggg tagagttcaa tttgaaactg acacagatca
6181 tgattttgaa gctaatcaaa acacaaagtt caccccagtc ggtgtcatcc aagatggtag
6241 caccacccac cgaaacgaac cccaacagtg ggtgctccca agttactcag gcagaaatac
6301 tcacaatgta catttggccc ccgctgtagc ccccaccttt ccgggtgagc aactcctctt
6361 tttcagatcc accatgcccg gatgcagcgg gtaccccaac atggatttgg actgtctgct
6421 cccccaggaa tgggtgcagt acttctacca agaggcagcc ccagcacaat ctgatgtggc
6481 tctgctaaga tttgtgaatc cagacacagg tagggttttg tttgagtgca agcttcacaa
6541 atcaggctat gttacagtgg cccacactgg ccaacatgac ttggttatcc cccccaatgg
6601 ttactttagg tttgattcct gggtcaacca gttctacacg cttgccccca tgggaaatgg
6661 aacggggcgt agacgtgcag tataatggct ggagctttct ttgctggatt ggcatctgat
6721 gtccttggct ctggacttgg ttcccttatc aatgctggag ctggggccat taaccaaaaa
6781 gttgaatttg aaaataacag aaaattgcaa caagcgtcct tccaatttag cagcaatctg
6841 caacaggctt ccttccaaca tgataaagag atgctccaag cacaaattga ggccaccaaa
6901 aagctacaac aggaaatgat gaaagttaag caggcaatgc tcctagaggg tgggttctct
6961 gagacagatg cagcccgcgg ggcaattaac gcccccatga caaaagcttt ggactggagc
7021 gggacaaggt actgggctcc agatgctagg attacaacat acaatgcagg ccatttttcc
7081 acccctcaac catcgagggc actgccagga agagctaatc ttagggatgc tgtccctgct
7141 cggggaccct ccaacaaatc ttctaactct tctactgtca cctctgtgta ttcaaatcaa
7201 actatttcaa cgagacttgg ttctacagct ggttctggaa ccagtgtctc gagcctcccg
7261 tcaactgcaa ggactaggag ttgggttgag gatcaaaata ggaatttgtc acctttcatg
7321 aggggggccc acaacatatc atttgtcacc ccaccatcta gcagatcctc tagccaaggc
7381 acagtctcaa ccgtgcctaa agagattttg gactcctgga ctggcgcttt caacacgcgc
7441 aggcagcctc tcttcgctca cattcgtaag cgaggggagt cacgggtgta a
//